Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000463745
Querying Taster for transcript #2: ENST00000335979
Querying Taster for transcript #3: ENST00000394206
MT speed 0 s - this script 4.837854 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ARL6disease_causing_automatic0.999999222727388simple_aaeaffected0L170Wsingle base exchangers104893681show file
ARL6disease_causing_automatic0.999999222727388simple_aaeaffected0L170Wsingle base exchangers104893681show file
ARL6disease_causing_automatic0.999999222727388simple_aaeaffected0L170Wsingle base exchangers104893681show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999222727388 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042297)
  • known disease mutation: rs2043 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510644T>GN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000463745
Genbank transcript ID N/A
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.509T>G
cDNA.986T>G
g.27280T>G
AA changes L170W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 170
frameshift no
known variant Reference ID: rs104893681
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2043 (pathogenic for Bardet-Biedl syndrome 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4770.99
4.2881
(flanking)0.4011
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased27282wt: 0.6748 / mu: 0.6806 (marginal change - not scored)wt: GCTTGCAAGAAGGTG
mu: GCTGGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.99wt: AAGGCTTGCAAGAAG
mu: AAGGCTGGCAAGAAG		 GGCT|tgca
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      170ICASDAIKGEGLQEGVDWLQDQIQ
mutated  not conserved    170ICASDAIKGEGWQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  170ICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  170ICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  170ICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  169ICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  170ICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  172ICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  170IHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
170180HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 1038 / 1038
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 478 / 478
chromosome 3
strand 1
last intron/exon boundary 1013
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 509
cDNA position
(for ins/del: last normal base / first normal base)		 986
gDNA position
(for ins/del: last normal base / first normal base)		 27280
chromosomal position
(for ins/del: last normal base / first normal base)		 97510644
original gDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered gDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
original cDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered cDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGW QEGVDWLQDQ
IQTVKT*
speed 1.30 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999222727388 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042297)
  • known disease mutation: rs2043 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510644T>GN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000335979
Genbank transcript ID NM_032146
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.509T>G
cDNA.862T>G
g.27280T>G
AA changes L170W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 170
frameshift no
known variant Reference ID: rs104893681
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2043 (pathogenic for Bardet-Biedl syndrome 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4770.99
4.2881
(flanking)0.4011
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased27282wt: 0.6748 / mu: 0.6806 (marginal change - not scored)wt: GCTTGCAAGAAGGTG
mu: GCTGGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.99wt: AAGGCTTGCAAGAAG
mu: AAGGCTGGCAAGAAG		 GGCT|tgca
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      170ICASDAIKGEGLQEGVDWLQDQIQ
mutated  not conserved    170ICASDAIKGEGWQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  170ICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  170ICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  170ICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  169ICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  170ICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  172ICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  170IHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
170180HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 914 / 914
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 354 / 354
chromosome 3
strand 1
last intron/exon boundary 889
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 509
cDNA position
(for ins/del: last normal base / first normal base)		 862
gDNA position
(for ins/del: last normal base / first normal base)		 27280
chromosomal position
(for ins/del: last normal base / first normal base)		 97510644
original gDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered gDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
original cDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered cDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGW QEGVDWLQDQ
IQTVKT*
speed 1.44 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999222727388 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042297)
  • known disease mutation: rs2043 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:97510644T>GN/A show variant in all transcripts   IGV
HGNC symbol ARL6
Ensembl transcript ID ENST00000394206
Genbank transcript ID NM_177976
UniProt peptide Q9H0F7
alteration type single base exchange
alteration region CDS
DNA changes c.509T>G
cDNA.822T>G
g.27280T>G
AA changes L170W Score: 61 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 170
frameshift no
known variant Reference ID: rs104893681
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2043 (pathogenic for Bardet-Biedl syndrome 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042297)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4770.99
4.2881
(flanking)0.4011
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased27282wt: 0.6748 / mu: 0.6806 (marginal change - not scored)wt: GCTTGCAAGAAGGTG
mu: GCTGGCAAGAAGGTG		 TTGC|aaga
Donor increased27279wt: 0.70 / mu: 0.99wt: AAGGCTTGCAAGAAG
mu: AAGGCTGGCAAGAAG		 GGCT|tgca
distance from splice site 27
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      170ICASDAIKGEGLQEGVDWLQDQIQ
mutated  not conserved    170ICASDAIKGEGWQEGVDWLQDQ
Ptroglodytes  all identical  ENSPTRG00000015139  170ICASDAIKGEGLQEGVDWLQDQ
Mmulatta  all identical  ENSMMUG00000023332  170ICASDAIKGEGLQEGVDWLQDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022722  170ICASDAIKGEGLQEGVDWLQEK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000017239  169ICATDALKGEGLQEGVDWLQDQ
Drerio  all identical  ENSDARG00000032056  170ICASDAVKGEGLLEGVDWLQDQ
Dmelanogaster  all identical  FBgn0034446  172ICSSSAISGEGLGEGVQWLI
Celegans  all identical  C38D4.8  170IHSTCALTGDGLDKAMQQLSAE
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
170180HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 561 / 561
position (AA) of stopcodon in wt / mu AA sequence 187 / 187
position of stopcodon in wt / mu cDNA 874 / 874
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 314 / 314
chromosome 3
strand 1
last intron/exon boundary 849
theoretical NMD boundary in CDS 485
length of CDS 561
coding sequence (CDS) position 509
cDNA position
(for ins/del: last normal base / first normal base)		 822
gDNA position
(for ins/del: last normal base / first normal base)		 27280
chromosomal position
(for ins/del: last normal base / first normal base)		 97510644
original gDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered gDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
original cDNA sequence snippet TGCCATAAAAGGAGAAGGCTTGCAAGAAGGTGTAGACTGGC
altered cDNA sequence snippet TGCCATAAAAGGAGAAGGCTGGCAAGAAGGTGTAGACTGGC
wildtype AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGL QEGVDWLQDQ
IQTVKT*
mutated AA sequence MGLLDRLSVL LGLKKKEVHV LCLGLDNSGK TTIINKLKPS NAQSQNILPT IGFSIEKFKS
SSLSFTVFDM SGQGRYRNLW EHYYKEGQAI IFVIDSSDRL RMVVAKEELD TLLNHPDIKH
RRIPILFFAN KMDLRDAVTS VKVSQLLCLE NIKDKPWHIC ASDAIKGEGW QEGVDWLQDQ
IQTVKT*
speed 1.36 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

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